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Aliases for PSPH Gene

Aliases for PSPH Gene

  • Phosphoserine Phosphatase 2 3 5
  • O-Phosphoserine Phosphohydrolase 3 4
  • L-3-Phosphoserine Phosphatase 3 4
  • EC 3.1.3.3 4 63
  • PSPase 3 4
  • PSP 3 4
  • PSPHD 3

External Ids for PSPH Gene

Previous HGNC Symbols for PSPH Gene

  • PSP

Previous GeneCards Identifiers for PSPH Gene

  • GC07M055542
  • GC07M055785
  • GC07M055820
  • GC07M055853
  • GC07M055892

Summaries for PSPH Gene

Entrez Gene Summary for PSPH Gene

  • The protein encoded by this gene belongs to a subfamily of the phosphotransferases. This encoded enzyme is responsible for the third and last step in L-serine formation. It catalyzes magnesium-dependent hydrolysis of L-phosphoserine and is also involved in an exchange reaction between L-serine and L-phosphoserine. Deficiency of this protein is thought to be linked to Williams syndrome. [provided by RefSeq, Jul 2008]

GeneCards Summary for PSPH Gene

PSPH (Phosphoserine Phosphatase) is a Protein Coding gene. Diseases associated with PSPH include phosphoserine phosphatase deficiency and 3-phosphoserine phosphatase deficiency. Among its related pathways are Metabolism and Carbon metabolism. GO annotations related to this gene include calcium ion binding and magnesium ion binding.

UniProtKB/Swiss-Prot for PSPH Gene

  • Catalyzes the last step in the biosynthesis of serine from carbohydrates. The reaction mechanism proceeds via the formation of a phosphoryl-enzyme intermediates.

Gene Wiki entry for PSPH Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PSPH Gene

Genomics for PSPH Gene

Regulatory Elements for PSPH Gene

Promoters for PSPH Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PSPH on UCSC Golden Path with GeneCards custom track

Genomic Location for PSPH Gene

Chromosome:
7
Start:
56,010,363 bp from pter
End:
56,051,604 bp from pter
Size:
41,242 bases
Orientation:
Minus strand

Genomic View for PSPH Gene

Genes around PSPH on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PSPH Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PSPH Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PSPH Gene

Proteins for PSPH Gene

  • Protein details for PSPH Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P78330-SERB_HUMAN
    Recommended name:
    Phosphoserine phosphatase
    Protein Accession:
    P78330
    Secondary Accessions:
    • B2RCR5
    • Q7Z3S5

    Protein attributes for PSPH Gene

    Size:
    225 amino acids
    Molecular mass:
    25008 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for PSPH Gene

neXtProt entry for PSPH Gene

Proteomics data for PSPH Gene at MOPED

Selected DME Specific Peptides for PSPH Gene

Post-translational modifications for PSPH Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

Domains & Families for PSPH Gene

Gene Families for PSPH Gene

Protein Domains for PSPH Gene

Suggested Antigen Peptide Sequences for PSPH Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P78330

UniProtKB/Swiss-Prot:

SERB_HUMAN :
  • Belongs to the SerB family.
Family:
  • Belongs to the SerB family.
genes like me logo Genes that share domains with PSPH: view

Function for PSPH Gene

Molecular function for PSPH Gene

GENATLAS Biochemistry:
phosphoserine phosphatase,catalyzing the last step of serine biosynthesis
UniProtKB/Swiss-Prot CatalyticActivity:
O-phospho-L(or D)-serine + H(2)O = L(or D)-serine + phosphate.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by calcium ions.
UniProtKB/Swiss-Prot Function:
Catalyzes the last step in the biosynthesis of serine from carbohydrates. The reaction mechanism proceeds via the formation of a phosphoryl-enzyme intermediates.

Enzyme Numbers (IUBMB) for PSPH Gene

Gene Ontology (GO) - Molecular Function for PSPH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004647 phosphoserine phosphatase activity IEA,TAS --
genes like me logo Genes that share ontologies with PSPH: view
genes like me logo Genes that share phenotypes with PSPH: view

Human Phenotype Ontology for PSPH Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PSPH Gene

MGI Knock Outs for PSPH:
  • Psph tm1.1(KOMP)Vlcg
  • Psph tm1a(EUCOMM)Hmgu

Animal Model Products

No data available for Transcription Factor Targets and HOMER Transcription for PSPH Gene

Localization for PSPH Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PSPH Gene COMPARTMENTS Subcellular localization image for PSPH gene
Compartment Confidence
cytosol 5
cytoskeleton 3
mitochondrion 1
nucleus 1
plasma membrane 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for PSPH Gene

Pathways & Interactions for PSPH Gene

genes like me logo Genes that share pathways with PSPH: view

UniProtKB/Swiss-Prot P78330-SERB_HUMAN

  • Pathway: Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 3/3.

Gene Ontology (GO) - Biological Process for PSPH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006563 L-serine metabolic process IDA 15291819
GO:0006564 L-serine biosynthetic process IEA,TAS --
GO:0009612 response to mechanical stimulus IEA --
GO:0016311 dephosphorylation IEA,TAS --
GO:0034641 cellular nitrogen compound metabolic process TAS --
genes like me logo Genes that share ontologies with PSPH: view

No data available for SIGNOR curated interactions for PSPH Gene

Drugs & Compounds for PSPH Gene

(8) Drugs for PSPH Gene - From: HMDB, Novoseek, and DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Serine Approved Nutra Full agonist, Agonist 0
D-2-Amino-3-Phosphono-Propionic Acid Experimental Pharma Target 0
D-serine Experimental Pharma Agonist 0
Magnesium Nutra 0

(7) Additional Compounds for PSPH Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
phosphoserine
  • 3-O-Phosphoserine
  • Dexfosfoserine
  • Fosforina
  • L-3-Phosphoserine
  • L-O-Phosphoserine
407-41-0
DL-O-Phosphoserine
  • 3-Phospho-1-serine
  • 3-Phospho-serine
  • 3-Phosphoserine
  • DL-O-Phosphorylserine
  • DL-O-Phosphoserine
17885-08-4
Phosphate
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)
14265-44-2
phosphoric acid
  • Acide phosphorique (FRENCH)
  • Acido fosforico [Italian]
  • Acidum phosphoricum
  • Diphosphate tetrasodium
  • Fosforzuuroplossingen [Dutch]
7664-38-2
Water
  • Dihydrogen oxide
  • Steam
7732-18-5
genes like me logo Genes that share compounds with PSPH: view

Transcripts for PSPH Gene

Unigene Clusters for PSPH Gene

Phosphoserine phosphatase:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PSPH Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g · 1h ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7a · 7b · 7c · 7d · 7e · 7f ^ 8 ^ 9 ^ 10 ^ 11a · 11b ·
SP1: - - -
SP2: - - - - - - - - -
SP3: -
SP4: -
SP5: - -
SP6: -
SP7: - - - - - - - - -
SP8:
SP9: - - - - - - - - - - -
SP10: - - - - - - - - - -
SP11: - - - - - - - - - - -
SP12: - - - - - - - - -
SP13: - - - - - - - - - -
SP14: - - - - - - - - -
SP15: - - - - - - - - -
SP16: - - - - - - - - -
SP17: - - - - - - - - - - - - - -
SP18: - - - - - - - -
SP19: - - - - -
SP20:
SP21: - - - - - - -
SP22: - - - - - - - - -
SP23: - - - - - - - - - -
SP24:
SP25: -

ExUns: 11c · 11d · 11e ^ 12a · 12b · 12c · 12d ^ 13a · 13b ^ 14 ^ 15a · 15b
SP1: -
SP2: -
SP3:
SP4: -
SP5: -
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17: -
SP18:
SP19: - - - - - - - - -
SP20:
SP21:
SP22:
SP23:
SP24:
SP25:

Relevant External Links for PSPH Gene

GeneLoc Exon Structure for
PSPH
ECgene alternative splicing isoforms for
PSPH

Expression for PSPH Gene

mRNA expression in normal human tissues for PSPH Gene

Protein differential expression in normal tissues from HIPED for PSPH Gene

This gene is overexpressed in Fetal gut (11.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PSPH Gene



SOURCE GeneReport for Unigene cluster for PSPH Gene Hs.512656

genes like me logo Genes that share expression patterns with PSPH: view

Protein tissue co-expression partners for PSPH Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PSPH Gene

Orthologs for PSPH Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PSPH Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PSPH 36
  • 99 (a)
OneToOne
PSPH 35
  • 99.7 (n)
  • 99.11 (a)
cow
(Bos Taurus)
Mammalia PSPH 36
  • 94 (a)
OneToOne
PSPH 35
  • 90.96 (n)
  • 94.22 (a)
dog
(Canis familiaris)
Mammalia PSPH 35
  • 91.26 (n)
  • 95.11 (a)
PSPH 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Psph 16
Psph 36
  • 94 (a)
OneToOne
Psph 35
  • 86.96 (n)
  • 93.78 (a)
oppossum
(Monodelphis domestica)
Mammalia PSPH 36
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PSPH 36
  • 76 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Psph 35
  • 86.52 (n)
  • 94.67 (a)
chicken
(Gallus gallus)
Aves PSPH 36
  • 80 (a)
OneToOne
PSPH 35
  • 73.63 (n)
  • 80 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia psph 35
  • 74.11 (n)
  • 80.8 (a)
Str.15388 35
zebrafish
(Danio rerio)
Actinopterygii psph 35
  • 64.89 (n)
  • 69.78 (a)
psph 36
  • 69 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012247 35
  • 53.86 (n)
  • 49.54 (a)
fruit fly
(Drosophila melanogaster)
Insecta aay 36
  • 40 (a)
OneToOne
aay 35
  • 55.61 (n)
  • 50.93 (a)
worm
(Caenorhabditis elegans)
Secernentea Y62E10A.13 36
  • 41 (a)
OneToOne
Y62E10A.13a 37
  • 50 (a)
Y62E10A.13b 37
  • 50 (a)
Y62E10A.13c 37
  • 49 (a)
Y62E10A.13 35
  • 55 (n)
  • 52.27 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SER2 36
  • 19 (a)
OneToOne
SER2 38
thale cress
(Arabidopsis thaliana)
eudicotyledons PSP 35
  • 53.72 (n)
  • 50.45 (a)
rice
(Oryza sativa)
Liliopsida Os12g0502400 35
  • 56.65 (n)
  • 50.7 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1610 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 53 (a)
OneToOne
Species with no ortholog for PSPH:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PSPH Gene

ENSEMBL:
Gene Tree for PSPH (if available)
TreeFam:
Gene Tree for PSPH (if available)

Paralogs for PSPH Gene

(1) SIMAP similar genes for PSPH Gene using alignment to 4 proteins:

Pseudogenes.org Pseudogenes for PSPH Gene

genes like me logo Genes that share paralogs with PSPH: view

No data available for Paralogs for PSPH Gene

Variants for PSPH Gene

Sequence variations from dbSNP and Humsavar for PSPH Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
VAR_022378 Phosphoserine phosphatase deficiency (PSPHD)
VAR_022379 Phosphoserine phosphatase deficiency (PSPHD)
rs2016724 -- 56,043,073(-) ccagg(C/G)tggtc intron-variant
rs2002651 -- 56,042,077(+) aatta(C/G)caggg intron-variant
rs2002693 -- 56,043,110(-) tttgt(A/G)ttttt intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PSPH Gene

Variant ID Type Subtype PubMed ID
esv28230 CNV Gain+Loss 19812545
esv2734447 CNV Deletion 23290073
dgv1201e199 CNV Deletion 23128226
nsv888064 CNV Gain 21882294
esv2734448 CNV Deletion 23290073
esv1571450 CNV Insertion 17803354
dgv1106n67 CNV Gain 20364138
nsv819501 CNV Gain 19587683
dgv1107n67 CNV Gain 20364138
nsv824122 CNV Gain 20364138

Variation tolerance for PSPH Gene

Residual Variation Intolerance Score: 90.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.35; 26.79% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PSPH Gene

HapMap Linkage Disequilibrium report
PSPH
Human Gene Mutation Database (HGMD)
PSPH

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PSPH Gene

Disorders for PSPH Gene

MalaCards: The human disease database

(10) MalaCards diseases for PSPH Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
phosphoserine phosphatase deficiency
  • phosphoserine phosphatase
3-phosphoserine phosphatase deficiency
lacrimal gland carcinoma
  • carcinoma of the lacrimal gland
psph deficiency
  • phosphoserine phosphatase deficiency
lacrimal gland adenocarcinoma
  • adenocarcinoma of lacrimal gland
- elite association - COSMIC cancer census association via MalaCards
Search PSPH in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SERB_HUMAN
  • Phosphoserine phosphatase deficiency (PSPHD) [MIM:614023]: A disorder that results in pre- and postnatal growth retardation, moderate psychomotor retardation and facial features suggestive of Williams syndrome. {ECO:0000269 PubMed:14673469}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PSPH

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PSPH
genes like me logo Genes that share disorders with PSPH: view

No data available for Genatlas for PSPH Gene

Publications for PSPH Gene

  1. Human L-3-phosphoserine phosphatase: sequence, expression and evidence for a phosphoenzyme intermediate. (PMID: 9188776) Collet J.-F. … Van Schaftingen E. (FEBS Lett. 1997) 2 3 4 67
  2. High-resolution structure of human phosphoserine phosphatase in open conformation. (PMID: 12777757) Peeraer Y. … De Ranter C. (Acta Crystallogr. D 2003) 3 23
  3. Purification, crystallization and preliminary X-ray diffraction analysis of human phosphoserine phosphatase. (PMID: 11752790) Peeraer Y. … De Ranter C. (Acta Crystallogr. D Biol. Crystallogr. 2002) 3 23
  4. Molecular basis for the local conformational rearrangement of human phosphoserine phosphatase. (PMID: 12213811) Kim H.Y. … Hwang K.Y. (J. Biol. Chem. 2002) 3 23
  5. Mechanistic studies of phosphoserine phosphatase, an enzyme related to P-type ATPases. (PMID: 10567362) Collet J.F. … Van Schaftingen E. (J. Biol. Chem. 1999) 3 23

Products for PSPH Gene

Sources for PSPH Gene

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